Since the recognition of mitochondrial diseases in humans in 1962 [1], numerous studies have elucidated the physiological and pathological significance of mitochondrial function. Mitochondria are intracellular organelles, which are present in almost every cell in the body and are responsible for the production of energy in the form of adenosine triphosphate (ATP) [2,3]. Thus, in patients with mitochondrial diseases, organs that are dependent on mitochondrial production for energy may be damaged [4]. In the neonatal period, a “triad” of cerebromuscular (e.g., recurrent apnea, inactivity, convulsions, and hypotonia), gastrointestinal and hepatic (e.g., vomiting, poor feeding, diarrhea, and hepatomegaly), and myocardial symptoms (e.g., arrhythmias, cardiomyopathy, and heart failure) related to mitochondrial diseases have been reported [5]. In infancy, symptoms of mitochondrial diseases include poor weight gain, progressive liver damage, cerebellar ataxia, pyramidal tract signs, psychomotor disturbances, respiratory failure, myotonia, and amino aciduria [6,7]. Central nervous system symptoms and muscular symptoms of mitochondrial diseases occur during childhood and adulthood. Three major mitochondrial encephalomyopathies have been reported: mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes [8,9,10]; myoclonic epilepsy and ragged-red fiber disease [11,12]; and chronic progressive external ophthalmoplegia, including Kearns–Sayre syndrome [13,14,15]. As the pathogenesis of mitochondrial disease suggests, the pathological significance of mitochondrial dysfunction is enormous. Mitochondrial dysfunction is also a hallmark of biological aging, as mitochondrial dysfunction worsens with age [16].

In eukaryotic cells, nuclear DNA (nDNA) and mitochondrial DNA (mtDNA) cooperate to regulate cellular functions [17]. Human mtDNA comprises a cyclic multicopy genome containing 16,569 base pairs, with usually tens to thousands of copies per cell. Human mtDNA is maternally inherited, as paternal mitochondria in fertilized eggs are removed by “mitophagy” [18,19]. Mitophagy, a quality control mechanism, is the selective degradation of mitochondria by autophagy for maintaining the health of the mitochondrial network [20,21]. Human mtDNA is independently replicated, and each genome mutates on its own, resulting in the formation of a condition called “heteroplasmy” [22,23]. Heteroplasmy means the existence of a normal version of the maternal mtDNA genome and a version of the genome containing a mutation, and this mixing rate easily changes as cells proliferate and differentiate. The mode of existence of human mtDNA also differs among tissues [24]. For example, mtDNA exists in single circles in many organs and cells, but in the heart, several mtDNA molecules are linked together in a complex network. The fact that the mode of existence of mtDNA differs in each tissue may be a consequence of the search for the most suitable state to maintain mtDNA in each tissue. While the mitochondrial genome is considerably smaller than that of the nuclear genome, the mRNA transcribed from mtDNA accounts for about 30% of total cellular mRNA in the heart and 5–25% of total cellular mRNA in other organs [25]. After being transcribed, mitochondrial RNA is processed, the mitoribosome is assembled, and respiratory chain proteins encoded by mtDNA are synthesized [26]. Human mtDNA at the population level is shaped by selective forces within the female germ line under nuclear genetic control [27]. According to the literature, the incidence of mitochondrial diseases is 9.6 per 100,000, of which 1.2 to 1.5 patients have a single mtDNA deletion [28,29,30]. The majority of mitochondrial diseases are inherited through autosomal or X-linked inheritance rather than maternal inheritance, and around 75% of mitochondrial diseases, especially those that occur in childhood, are caused by nDNA mutations [6,31]. Around 300 causative genes of human mitochondrial diseases have been identified using next-generation sequencing [32]. In an animal study, investigators removed the nucleus from a fertilized egg of a mouse with an mtDNA mutation and transplanted it into an unfertilized egg of a healthy female mouse [33]. In this study, the resulting litter was healthy. However, as mentioned above, such a technical approach would only be applicable to a subset of patients with mitochondrial diseases. In terms of the drug delivery system (DDS), which delivers target molecules to mitochondria, various attempts have been made to protect or activate mitochondrial functions [34]. Mitochondrial transplantation treatment [34,35] is one of these treatment challenges, but several issues remain to be addressed [35,36,37].

As shown in previous studies, the number of mtDNA copies in the peripheral blood decreases with age [38], and the decrease is negatively associated with age-related events, such as all-cause mortality [39]. In addition, mtDNA copy number loss is associated with cognitive function [40], cardiovascular diseases [41], and infectious morbidity and mortality in patients with chronic kidney disease [42]. Mitochondrial DNA depletion syndrome (MTDPS) refers to diseases in which the mtDNA copy number is reduced, and mitochondrial energy metabolism is impaired [43]. The underlying pathogenesis of MTDPS refers to abnormalities in genes related to the replication maintenance mechanism of mtDNA encoded in nDNA, resulting not only in mtDNA depletion but also in multiple deletions and point mutations [44]. These include abnormalities in POLG, POLG2, Twinkle, RNASEH1, DNA2, and MGME1 genes [45]. The mode of inheritance of MTDPS is autosomal recessive [46]. As suggested by MTDPS associated with a variety of pathological conditions, dysregulation of mtDNA copy number and mitochondrial dysfunction play a role in a variety of pathologies. The maintenance of mtDNA copy number via mtDNA replication is of high importance not only at the cellular level but also at the individual level.

In terms of its physiological significance, mtDNA copy number is important from fetal, through infantile and childhood stages, to adulthood. In fact, mtDNA copy number influences early developmental cell differentiation and reprogramming of induced pluripotent stem cells [47]. In a previous study, the mtDNA contents of newborns with abnormal birth weights were lower than those of newborns with normal weights [48]. Based on accumulating evidence [49,50,51], reduced mtDNA content may be a putative link between abnormal fetal growth and metabolic and cardiovascular complications in later life. In a recent population-based follow-up study of middle-aged Swedish women (N = 2387), the mtDNA copy number was significantly lower both in women with type 2 diabetes and in those who developed type 2 diabetes during the follow-up period compared to those who did not develop type 2 diabetes [52]. Furthermore, a study based on data from the U.K. Biobank confirmed that a higher mtDNA copy number was significantly associated with a lower prevalence of neurodegenerative diseases (odds ratio (OR) = 0.89, confidence interval (CI) = 0.83; 0.96) and a lower incidence rate of neurodegenerative diseases (hazard ratio = 0.95, 95% CI = 0.91; 0.98) [53].

The Developmental Origin of Health and Disease (DOHaD)” theory posits that environmental factors during development act as risk factors for health and disease in adulthood [54,55,56,57,58,59,60]. Considering the physiological and pathological significance of mtDNA copy number from the perspective of DOHaD theory could shed light on the potential role of mtDNA copy number as a biomarker of disease in later life [61]. This paper discusses the potential of mtDNA copy number in early life as a biomarker of health and disease in later life (Figure 1), focusing on recent epidemiological studies that suggest a correlation between environmental factors and mtDNA copy number changes during the fetal period.